[Bioc-devel] coverage(gr, weight='score') does not work when score(gr) is an Rle

[Michael Lawrence]

Sorry, I was confused. You're right, there's not much point in keeping it
compressed.

On Fri, Apr 17, 2015 at 10:14 AM, Hervé Pagès <hpages at fredhutch.org> wrote:

> On 04/17/2015 10:00 AM, Michael Lawrence wrote:
>
>> Is that the case here? He has an Rle as an mcol in the GRanges, so in
>> general expanding it will not align with the other components.
>>
>
> Not sure what you mean. Can you give an example?
>
> H.
>
>
>> On Fri, Apr 17, 2015 at 9:42 AM, Hervé Pagès <hpages at fredhutch.org
>> <mailto:hpages at fredhutch.org>> wrote:
>>
>>     Hi,
>>
>>     I think we should just expand the Rle internally. That will produce
>>     a numeric vector of the length of the GRanges i.e. it will be the
>>     same size as the start and end components of the GRanges object
>> itself.
>>     No big deal at all.
>>
>>     I'll make that change.
>>
>>     H.
>>
>>
>>     On 04/17/2015 09:00 AM, Michael Lawrence wrote:
>>
>>         Ideally it should be supported, but it would take some work as
>>         the coverage
>>         stuff is all in C. Could you give more details on your use case?
>> For
>>         example, if you already have a range for every position on the
>>         chromosome,
>>         you could just extract the score column. I'm guessing it's more
>>         complicated
>>         than that. If the zeros are the problem, you could just subset
>>         the GRanges
>>         to remove the ranges with zero score, and then coerce the score
>>         to numeric
>>         before calling coverage.
>>
>>         Michael
>>
>>         2015-04-17 8:00 GMT-07:00 Philip Lijnzaad
>>         <p.lijnzaad at umcutrecht.nl <mailto:p.lijnzaad at umcutrecht.nl>>:
>>
>>
>>             Dear all,  I'm puzzled by the following behaviour:
>>
>>             Given
>>
>>                   n <- 10
>>                   gr <- GRanges(seqnames=Rle('A', n),
>>                                 ranges=IRanges(1:n, width=1),
>>                                 score=Rle(5,n))
>>             If I do
>>
>>                   coverage(gr,weight='score')
>>
>>             I get
>>
>>                   Error in .normarg_shift_or_weight(weight, "weight", x) :
>>                     'weight' must be a numeric vector, a single string,
>>             or a list-like
>>             object
>>
>>             Surely 'score' should be allowed to be an Rle? Especially
>>             given the
>>             fact that the return value of coverage(x,weight="score")
>>             when score is
>>             plain numeric vector is always an Rle ! Is this the expected
>>             behaviour?
>>             If so, I would argue that violates the principle of least
>>             suprise :-)
>>
>>             The background to this is that I do numerical analysis on
>>             derived
>>             numerical data along my chromosomes. It contains many
>>             contiguous zeroes so it would be wasteful to cast
>>             everything down using as.numeric().
>>
>>             This is R version 3.01 on x86_64 Linux, Bioconductor version
>>             2.13,
>>
>>                 package.version("IRanges")
>>
>>             [1] "1.20.7"
>>
>>                 package.version("GenomicRanges")
>>
>>             [1] "1.14.4"
>>
>>             Regards,
>>
>>
>>             Philip
>>
>>
>>             --
>>             Philip Lijnzaad, PhD
>>             Molecular Cancer Research
>>             University Medical Center (UMC), Utrecht
>>             Stratenum room 2.211
>>             IM: plijnzaad at jabber.org <mailto:plijnzaad at jabber.org> ,
>>             philip.lijnzaad at gmail.com <mailto:philip.lijnzaad at gmail.com>
>>             P.O. Box 85060, 3508 AB Utrecht
>>             (Universiteitsweg 100, 3584 CG Utrecht)
>>             The Netherlands
>>             tel: +31 (0)8875 68464 <tel:%2B31%20%280%298875%2068464>
>>
>>
>>
>> ------------------------------------------------------------------------------
>>
>>             De informatie opgenomen in dit bericht kan vertrouwelijk
>>             zijn en is
>>             uitsluitend bestemd voor de geadresseerde. Indien u dit
>>             bericht onterecht
>>             ontvangt, wordt u verzocht de inhoud niet te gebruiken en de
>>             afzender
>>             direct
>>             te informeren door het bericht te retourneren. Het
>>             Universitair Medisch
>>             Centrum Utrecht is een publiekrechtelijke rechtspersoon in
>>             de zin van de
>>             W.H.W.
>>             (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat
>>             geregistreerd
>>             bij
>>             de Kamer van Koophandel voor Midden-Nederland onder nr.
>>             30244197.
>>
>>             Denk s.v.p aan het milieu voor u deze e-mail afdrukt.
>>
>>
>>
>> ------------------------------------------------------------------------------
>>
>>             This message may contain confidential information and
>>             ...{{dropped:10}}
>>
>>
>>         _______________________________________________
>>         Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>
>>         mailing list
>>         https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>>     --
>>     Hervé Pagès
>>
>>     Program in Computational Biology
>>     Division of Public Health Sciences
>>     Fred Hutchinson Cancer Research Center
>>     1100 Fairview Ave. N, M1-B514
>>     P.O. Box 19024
>>     Seattle, WA 98109-1024
>>
>>     E-mail: hpages at fredhutch.org <mailto:hpages at fredhutch.org>
>>     Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
>>     Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>>
>>
>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>

	[[alternative HTML version deleted]]